SPIN/MPO manu

Date: 2022/09/16

Goal:

Summarize the story of SPIN/MPO.
Basics: C36m FF, Tip3P model, NPT ensemble, Langevin Thermo

Outline for input results

Details can be found in each sub-parts

OutL1. Folded vs. Unfolded Dissociation rate among SPIN/MPO

Reference: Xiaorong's simulation for unrestrained SPIN/MPO @ high T
Focus: If NTD dissociate faster. Point to next folded region constrain simulations.

OutL2. S.aureus vs. S.delphini Dissociation rate.

Reference: Yumeng's simulation for folded region restrained SPINs/MPO @450K, 40 rep

Focus:
a. dissociation rate line: intra/inter. two species. Fit function
b. psedo free energy surface.
c. part of discussion on coupled binding and folding.

OutL3. Physics basis of coupled binding and folding --- Hypothesis and validation.

Reference: Yumeng's simulation for SPIN-NTDs @300K, 20 rep

Focus:
a. dissociation rate line: *S.aureus vs. S.delphini. Fit function
b. Stability discussion towards the coupled binding and folding mechanism.

To Do List and Expectation

1. Organization of trajs from Xiaorong and Yumeng
2. Analysis
3. Write the manu

1. Folded (CTD) vs. Unfolded (NTD) SPIN Dissociation rate from MPO

From Xiaorong's email (2022/09/16):

Some of the trajectories are on rainier: 
/home/xrliu/work/research/14-spin/dissociate/s5-prod

And the rest are on pikes: 
/home/xrliu/work/research/14-spin/dissociate/s5-prod

System Setup

System:

S.aureus without heme
1. Xiaorong ran the simulations with cutted system:
~12 A proteins on MPO away from SPIN was deleted.
2. For native contacts visualization, Xiaorong made a good vmd file @
/home/xrliu/work/research/14-spin/dissociate/s1-model/view-native-contact.vmd
3. Temp she tried: {400 425 450 475 500}

Conclusion: (from README @ /home/xrliu/work/research/14-spin/dissociate/s5-prod)

400K: not dissociate within 100 ns
425K: not dissociate within 150 ns

450K-rep1:  dissociate within 87 ns --- NTD leave first
450K-rep2:  not dissociate within 400 ns, unfolding of SPIN C-terminal helices prevents the dissociation of hairpin
450K-rep3:  dissociate within 150 ns --- NTD unfold first, CTD dissociate
450K-rep4:  not dissociate within 400 ns
450K-rep5:  not dissociate within 450 ns
450K-rep6:  dissociate within 230 ns --- NTD leave first 
450K-rep7:  not dissociate within 400 ns
450K-rep8:  dissociate within 200 ns --- CTD leave first
450K-rep9:  not dissociate within 300 ns
450K-rep10: not dissociate within 300 ns
450K-rep11: dissociate within 55 ns --- NTD leave first!

475K: dissociate within 55 ns --- CTD first
500K-rep1: dissociate within 28 ns --- co-operatively
500K-rep2: dissociate within 33 ns --- Folded leave first

Conclusion

After visualizing all dissociation trajs, NTD does NOT always dissociate first even @ 450K. 
After analyzing, we may say that NTD dissociate faster than CTD...They are correlated.

450K: NTD dissociate faster than CTD

quick analysis below

Note:
1. The traj in xiaorong's dissociate folder is not successive, go to the original dcd:
    rep1 3 are in local, rainer, rep6 rep8 rep11 are in pikes

475-500K: CTD dissociate much faster than NTD

Main Results

1. The dissociation process is more correlated at the lower temperature.
2. Under the high temperature, the helix bundle will unfold and loss the binding ability...
3. With being well-structured, folded region seems to bind more strongly. Therefore, NTD may dissociate faster than CTD.

Yumeng's point: It is reasonable that CTD has faster dissociation rate under high T since it is more exposed.

2. S.aureus vs. S.delphini Dissociation rate.

Discussion Focus

In this part, we need to explore the main Question:
The dissociation (binding) mechanism of the two species.

We will show te above by two main figures:
a. The dissociation fit function for inter/intra rate
b. The dissociation mechanism

System

Two Species simulations:
/home/yumzhang/pikes_work/1-spin/spin/5uzu-spin/dissociate-heme/s5-rep
/home/yumzhang/pikes_work/1-spin/spin/6bmt-spin/dissociate-heme/s5-rep

Setup:
a. 40 reps 
b. 450K NPT
c. only NTD free (+ some loops on MPO)
d. Cutoff for contacts (i, i+3): 4.2A

Question

Data collect selection: 
shall we
1. collect the whole traj for all? 
2. Or the first 50 ns only for all? 
3. Or the dissociation part for dissociated reps? (and select for about 50 ns?) 

Yumeng's current selection: all traj's first 50 ns.
potential risk: bias from those undissociated traj... (a lot)

Another: shall we include bb in contact analysis?

Conclusion

1. S.aureus shows higher tendency to dissociate and unfold from complex than S.delphini.

Exponential Fit Function: $Q = a*e^{b*T}+c$

S.aureus

Dissociate:

$Q_{inter} = 0.29*e^{-0.12*T}+0.20$

Unfold:

$Q_{intra} = 0.27*e^{-0.12*T}+0.26$

S.delphini

Dissociate:

$Q_{inter} = 0.14*e^{-0.098*T}+0.34$

Unfold:

$Q_{intra} = 0.22*e^{-0.044*T}+0.51$

Notes:

  1. The coupled binding and folding mechanism:

    S.aureus: correlated coupled binding and folding.

    S.delphini: conformational selection (dissociate first then unfold).

  2. The NTD/MPO interactions are more dynamic for S.aureus

    Can be obtained both from the slope of dissociation and $Q_{inter}, $Q_{intra} after 50 ns.

2. The hairpin of S.delphini is more stable! Hard to unfold!

3. The binding mechanism:

S.aureus: correlated folding and binding

S.delphini: conformational selection

Dissociation analysis:

1. Each rep inter/intra dissociation rate (40)
2. Fitting line for inter/intra average 
3. Heatmap for mechanism exploring

2.1. Dissociation Per Rep

S.aureus

Sub-conclusions:

  1. Most replicas dissociate and unfold within 50ns in S.aureus/MPO complex.

  2. A few replicas unfold but not fully dissociate (4), while some others unbound but partially folded (3)

    However, reps in Cond_B and Cond_C actually show highly correlated unfolding and unbinding fractions.

  3. S.aureus/MPO is a less stable complex. And the dissociation is highly correlated with the unfolding process.

  4. Again, NTD of S.aureus is more dynamic.

S.delphini

Sub-conclusions:

  1. Most replicas keep bound and folded within 50ns in S.delphini/MPO complex.

  2. For those dissociated ones, most S.delphini-NTD keeps folded.

  3. S.delphini forms a more "stable" complex, and has very different dissociation process comparing to S.aureus.

  4. S.delphini prefers the conformational_selection mechanism.

2.2. Average Fit line

S.aureus

Conclusions

S.aureus

Dissociate:

$Q_{inter} = 0.29*e^{-0.12*T}+0.20$

Unfold:

$Q_{intra} = 0.27*e^{-0.12*T}+0.26$

Highly Correlated.

S.delphini

S.delphini

Dissociate:

$Q_{inter} = 0.14*e^{-0.098*T}+0.34$

Unfold:

$Q_{intra} = 0.22*e^{-0.044*T}+0.51$

Conformational Selection.

2.3 Free energy surface

(The saving frequence is a little large...)

S.aureus

S.delphini

3. The hairpin stability of S.aureus vs. S.delphini

Discussion Focus

In this part, we need to see if the dissociation related with the stability of the hairpin.

Pre_conclusion:

S.delphini has more stable NTD

System

Two Species simulations:
hairpin:
/home/yumzhang/pikes_work/1-spin/hairpinex1/5uzu/s5-20
/home/yumzhang/pikes_work/1-spin/hairpinex1/6bmt/s5-20

Setup:
a. 20 reps
b. 300K NPT
c. only 12 residues per hairpin from folded conformation

Question

contact including backbone should be considered or not

Conclusion

  1. S.aureus-NTD is easier to unfold.

  2. S.delphini-NTD can unfold faster... ?

S.aureus vs. S.delphini

S.aureus:

$Q_{NTD} = 0.39*e^{-0.04*T}+0.40$

S.delphini:

$Q_{NTD} = 0.35*e^{-0.15*T}+0.57$

Yumeng's point: we may need to kick out the folded replicas... Yumeng's results: does NOT work...

Stability analysis:

1. Each rep unfold rate (20)
2. Ave Fit line

3.1 Stability per rep

S.aureus

Sub-conclusions

  1. For S.aureus, 7/20 replicas unfold at 300K.

S.delphini

Sub-conclusions

  1. For S.delphini, there are 4/20 hairpin unfold within 50 ns.

3.2 Ave Stability

All 20 replicas

S.aureus and S.delphini together

S.aureus vs. S.delphini

S.aureus:

$Q_{NTD} = 0.39*e^{-0.04*T}+0.40$

S.delphini:

$Q_{NTD} = 0.35*e^{-0.15*T}+0.57$

Sub-conclusions

S.delphini has a tendency to unfold first but then become very stable...

Unfolded Replicas Solely

Since we have a pre-understanding that for 20 replicas, more unfolding events for S.aureus, we can then focus on these replicas solely.

S.aureus vs. S.delphini

S.aureus:

$Q_{NTD} = 0.65*e^{-0.07*T}+0.19$

S.delphini:

$Q_{NTD} = 0.75*e^{-0.13*T}+0.24$

Sub-conclusions

The unfolding process of S.delphini and S.aureus is very similar...

The specific selection of folded replicas does NOT work effectively...